Workflows
What is a Workflow?Filters
Tests The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool.
This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.
Type: Galaxy
Creators: Diana Chiang Jurado, Pavankumar Videm, Pablo Moreno
Submitter: WorkflowHub Bot
This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.
This workflow is used for GO and KEGG enrichment analysis using GOseq tools.
Workflow for variant analysis against a reference genome in GenBank format
Single-cell/nuclei pipeline for data derived from Oxford Nanopore
Pipeline to run and benchmark multiple sequence alignment tools.
